Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcgtcttgcttatacattgctcggctgctttcagttcgtttgattgatttctatccatgtgttgctgtgcgatatatgttaagctggaattttcttcttatcataccag

Basic information

species Zea mays
transcript GRMZM2G004932_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004932_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g44922.2 (Oryza sativa), 5'ss of exon 2
ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcgtcttgcttatacattgctcggctgctttcagttcgtttgattgatttctatccatgtgttgctgtgcgatatatgttaagctggaa-ttttcttcttatcat-accag
|||||||| ||||||||||||||||||||||||||||||||||||||||| ||||               ||| ||  |  ||||   ||  ||    | || |||   | |||  |  |||||   || ||| |  ||| || |||| |||||||| | | |||
ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtaaggct---------------ttgatcttccactttt--tttcttcttctaatatctgagcttgtaat-ttgtgc--catgtgtaatcctgaaacttttgttcttatcgttatcag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211119333|gb|FL065968.1|FL065968
EST:     ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
genomic: ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcg ... atcataccagGCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
EST: gi|71433707|gb|DR814757.1|DR814757
EST:     ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
genomic: ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcg ... atcataccagGCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
EST: gi|211119334|gb|FL065969.1|FL065969
EST:     ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAGTATTTTGCCNAATGAAGATGACACCGTTCCTCAAAAG
genomic: ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcg ... atcataccagGCAGTATTTTGTC-AATGAAGATGACACCGTTCCTCAAAAG
EST: gi|211119336|gb|FL065971.1|FL065971
EST:     ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
genomic: ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcg ... atcataccagGCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
EST: gi|211119335|gb|FL065970.1|FL065970
EST:     ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
genomic: ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcg ... atcataccagGCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
EST: gi|211118534|gb|FL065953.1|FL065953
EST:     ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
genomic: ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcg ... atcataccagGCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
EST: gi|211118536|gb|FL065955.1|FL065955
EST:     ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGGTTG
genomic: ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcg ... atcataccagGCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAGGTTG
EST: gi|211119328|gb|FL065963.1|FL065963
EST:     ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
genomic: ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcg ... atcataccagGCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
EST: gi|211119329|gb|FL065964.1|FL065964
EST:     ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
genomic: ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcg ... atcataccagGCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
EST: gi|211119337|gb|FL065972.1|FL065972
EST:     ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAGTATTTTGNCAATGAAGATGACACCGTTCCTCAAAAG
genomic: ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcg ... atcataccagGCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
EST: gi|211118531|gb|FL065950.1|FL065950
EST:     ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
genomic: ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcg ... atcataccagGCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
EST: gi|211118532|gb|FL065951.1|FL065951
EST:     ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
genomic: ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcg ... atcataccagGCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
EST: gi|211118537|gb|FL065956.1|FL065956
EST:     ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
genomic: ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcg ... atcataccagGCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
EST: gi|211119330|gb|FL065965.1|FL065965
EST:     ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
genomic: ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcg ... atcataccagGCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
EST: gi|211273595|gb|FL065975.1|FL065975
EST:     ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG
genomic: ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcg ... atcataccagGCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 172

ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcg ... atcataccagGCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 178

ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcg ... atcataccagGCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 225

ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcg ... atcataccagGCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 86

ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcg ... atcataccagGCAGTATTTTGTCAATGAAGATGACACCGTTCCTCAAAAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTATCCTAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtatggctcgtcttgcttatacattgctcggctgctttcagttcgtttgattgatttctatccatgtgttgctgtgcgatatatgttaagctggaattttcttcttatcataccag

- - - - - - - - - - AGATCA